The introduction of homogeneous HDL-C and LDL-C methods, which do not require the physical separation of lipoproteins, offer many practical advantages for routine clinical laboratory testing and are now widely utilized. The current guidelines for the diagnosis and treatment of cardiovascular disease, however, were based on older precipitation-based methods or were done by estimating LDL-C by the Friedewald equation. In this study, homogeneous HDL-C and LDL-C assays from 7 Japanese manufacturers and one global distributor were compared to the beta-quantification reference measurement procedure (RMP) and evaluated for precision, trueness, total error and specificity in subjects with relatively normal lipids, as well as in subjects with dyslipidemia and other conditions known to affect lipoprotein testing. Serum from 175 subjects from outpatient clinics or from inpatients with lipid disorders were collected. 37 (21%) had no known diseases and were not using lipid lowering drugs; the remaining 138 (79%) were being treated for cardiovascular disease, lipoprotein disorders or other diseases, such as kidney and liver disease. The 8 homogeneous assays were performed using a Roche/Hitachi 917 analyzer, according to the method described by each manufacturer. The RMP method was performed at the Centers for Disease Control and Prevention. All of the tests over a wide range of HDL-C and LDL-C values tested had a total CV of less than 4% and thus met the current National Cholesterol Education Program (NCEP) criteria for imprecision. The mean bias for the homogenous tests compared to RMP ranged from -5.2% to 4.9% for HDL-C and from -6.4% to 1.2% for LDL-C in non-disease subjects, but was -6.4% to 14.4% and -13.2% to 5% in dyslipidemic subjects for HDL-C and LDL-C tests, respectively. Because of the biases observed, particularly in dyslipidemic subjects, most of the homogenous tests did not reach the NCEP total error goal for HDL-C and LDL-C. In summary, the homogenous assays for HDL-C and LDL-C worked well in subjects with relatively normal lipids but due to non-specificity toward abnormal lipoproteins many of the methods did not perform as well in patients with dyslipidemias. For some rare genetic disorders of lipids, markedly discordant results were observed compared to the RMP. Future improvements are needed to extend the suitability of homogenous HDL-C and LDL-C assays for patients with dyslipidemias.